In pathology, images of tissue samples or cell smears are analyzed under a microscope. In histopathology, the pathologist studies tissue in order to come to a diagnosis. A tissue sample is a thin slice of tissue mounted between two glass slides. This tissue is not perfectly flat and typically not perfectly aligned with the focal plane of the imaging system. Besides that, the cells of the tissue are positioned at different heights in the tissue layer. Consequently, a significant part of the cells in a two-dimensional tissue image can be out of focus. The same goes for cytopathology images, where the pathologist analyzes loose cells with several cell nuclei. These cells are present in a thin layer of mounting fluid between two glass slides. Typically, these cells will not be positioned in a perfectly flat layer and the layer will not be perfectly aligned with the focal plane of the imaging system.
Y. Sun et. al describe in “Autofocusing Algorithm Selection in Computer Microscopy” in Intelligent Robots and Systems, 2005, how a focal plane that provides a desired focus for an object of interest can be computed.
Rough interpretation of the cell does not require perfect focus of all cells. However, at the point of the analysis where details of the cells need to be studied, proper focus of the cells at hand is required. The pathologist uses the fine focus knob of an analogue microscope to navigate to the right plane of the focus. Recent trends indicate that pathology might be digitized in the future. This means that image data might be obtained with a digital scanner and stored on a server. For a subset of applications, image data will be obtained for a single focal plane. Information obtained in this way can be compared to the current practice of using a normal microscope where the fine focus knob is removed. In such a situation, no adjustment of the focal situation is possible any more. Due to these technological changes, digital pathology data will be analyzed from a monitor or by a computer. While the importance of the focus adjustment remains equally important, the means for changing focus might substantially be different.